Capillary electrophoresis (CE) has been applied widely as an analytical technique because of several technical advantages: (i) capillaries have high surface-to-volume ratios which permit more efficient heat dissipation which, in turn, permit high electric fields to be used for more rapid separations; (ii) the technique requires minimal sample volumes; (iii) superior resolution of most analytes is attainable; and (iv) the technique is amenable to automation, e.g. Camilleri, editor, Capillary Electrophoresis Theory and Practice (CRC Press, Boca Raton, 1993); and Grossman et al, editors, Capillary Electrophoresis (Academic Press, San Diego, 1992). The need for rapid and accurate separation of nucleic acids, particularly DNA, arises in the analysis of polymerase chain reaction (PCR) products and DNA sequencing fragment analysis, e.g. Williams, Methods 4: 227-232 (1992); Drossman et al, Anal. Chem., 62: 900-903 (1990); Huang et al, Anal. Chem., 64: 2149-2154 (1992); and Swerdlow et al, Nucleic Acids Research, 18: 1415-1419 (1990).
Separation of DNA by denaturing CE with injection from high salt buffers, such as PCR buffer, often generates more than one target-specific peaks: a main peak migrating as single-stranded (ss) DNA and additional, faster-migrating peak or peaks, likely consisting of double-stranded (ds) or partially double-stranded DNA. The appearance of this artifactual peak(s), also referred to herein as a “shadow” or “shadow artifact” peak, presents problems for the assignment of peaks to nucleic acid species in the sample and for the quantitation of individual species therein.